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Correct GATK4 container spec #391

Merged
merged 1 commit into from
Jul 27, 2023
Merged

Correct GATK4 container spec #391

merged 1 commit into from
Jul 27, 2023

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adamrtalbot
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@adamrtalbot adamrtalbot commented Jul 27, 2023 •
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Updates nf-core/gatk4 container and removes prefix 'quay.io' that was breaking nf-core downloads.

Fixes nf-core/modules#3668 for this repo specifically.

PR checklist

  • This comment contains a description of changes (with reason).
  • If you've fixed a bug or added code that should be tested, add tests!
  • If you've added a new tool - have you followed the pipeline conventions in the contribution docs
  • If necessary, also make a PR on the nf-core/raredisease branch on the nf-core/test-datasets repository.
  • Make sure your code lints (nf-core lint).
  • Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
  • Ensure the test suite passes (nextflow run . -profile test_one_sample,docker --outdir <OUTDIR>).
  • Usage Documentation in docs/usage.md is updated.
  • Output Documentation in docs/output.md is updated.
  • CHANGELOG.md is updated.
  • README.md is updated (including new tool citations and authors/contributors).

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github-actions bot commented Jul 27, 2023 •
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nf-core lint overall result: Passed ✅ ⚠️

Posted for pipeline commit de8b2cc

+| ✅ 151 tests passed       |+
#| ❔   4 tests were ignored |#
!| ❗   1 tests had warnings |!

❗ Test warnings:

  • pipeline_todos - TODO string in awsfulltest.yml: You can customise AWS full pipeline tests as required

❔ Tests ignored:

  • files_exist - File is ignored: conf/modules.config
  • files_unchanged - File ignored due to lint config: .github/PULL_REQUEST_TEMPLATE.md
  • files_unchanged - File ignored due to lint config: .github/workflows/linting.yml
  • files_unchanged - File ignored due to lint config: .gitignore or .prettierignore or pyproject.toml

✅ Tests passed:

Run details

  • nf-core/tools version 2.9
  • Run at 2023-07-27 10:14:40

@adamrtalbot adamrtalbot mentioned this pull request Jul 27, 2023
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2 tasks
@adamrtalbot adamrtalbot merged commit f4d5d57 into nf-core:dev Jul 27, 2023
8 checks passed
@adamrtalbot adamrtalbot deleted the fix_gatk4_containers branch July 27, 2023 11:06
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@maxulysse maxulysse maxulysse approved these changes

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